Yes, young kittens like that don't really know any better, they forget where the litter box is and / or can't make it to the litter box because they can't hold it long enough like adult cats. It helps to keep a young kitten in one room, or if you let it roam the house have lots of litterboxes strategically placed around the house, preferably in rooms where she spends most of her time.
Some cats like separate boxes for pee and poop. Or won't go in again if it's been used once. I would try getting a second box and see what happens. You might also want to get some Kitten Attract litter.
It's possible that she has a UTI (Kobi had one at 14 weeks or so) and is just trying to get the message across to you. Ask the vet to do a urinalysis...that will tell you whether there is a medical or behavioral issue.